12:08 p.m.
Thanks for the help John and Dannon. I'll see if it works tomorrow. No need to raise a
trello card
Thanks
Neil
________________________________
From: Dannon Baker [dannon.baker(a)gmail.com]
Sent: Tuesday, August 05, 2014 11:14 PM
To: John Chilton
Cc: Burdett, Neil (DP&S, Herston - RBWH); galaxy-dev(a)lists.bx.psu.edu
Subject: Re: [galaxy-dev] error using get( $__user_id__ ) in xml file in new Galaxy
The method John suggests is definitely a better way to get the user's API key.
That said, the 'get' change is due to sqlalchemy version changes that happened
quite a while back. You can no longer 'get' directly from the model, you must use
a query object. So, for example, this line:
model.User.get( id )
Became:
sa_session.query( self.model.User).get( id )
Hope that gives a little context,
-Dannon
On Tue, Aug 5, 2014 at 8:56 AM, John Chilton
<jmchilton@gmail.com<mailto:jmchilton@gmail.com>> wrote:
Hmm...
The following should work for the last at least three releases I
think: ${__user__.api_keys[0].key}. Not sure why get/find are
unavailable on the User model class in the cheetah template now. I
think this version is a little better. Is this okay? If not I can
create a Trello card to investigate and restore the old functionality.
-John
On Tue, Aug 5, 2014 at 2:26 AM, <Neil.Burdett(a)csiro.au> wrote:
Hi,
I have recently upgraded Galaxy from a version I had last year. In my
tool xml file I could state:
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
in the <command> section to get the user's API. However, after updating to
the current version of Galaxy I get the following error when using this
entry in the xml file:
Traceback (most recent call last):
File "/home/bmladmin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 153, in prepare_job
job_wrapper.prepare()
File "/home/bmladmin/galaxy-dist/lib/galaxy/jobs/__init__.py", line 712,
in prepare
self.command_line, self.extra_filenames = tool_evaluator.build()
File "/home/bmladmin/galaxy-dist/lib/galaxy/tools/evaluation.py", line
348, in build
self.__build_command_line( )
File "/home/bmladmin/galaxy-dist/lib/galaxy/tools/evaluation.py", line
364, in __build_command_line
command_line = fill_template( command, context=param_dict )
File "/home/bmladmin/galaxy-dist/lib/galaxy/util/template.py", line 9, in
fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
"/home/bmladmin/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1407207170_7_53169.py",
line 92, in respond
NotFound: cannot find 'get' while searching for 'get'
Any ideas?
Thanks
Neil
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